Analysis of the algorithm: From kernels to backup genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
biological_process 1 134 6.999882332176266 11.432654770656663
cellular_component 1 40 4.162222345933308 5.25157343549579
disease 1 21 2.2250479846449136 2.909050012799259
interaction 1.0 729.0 29.8386134923593 54.03869234947398
molecular_function 1 26 3.0287856936832998 3.7159142158779024
pathway 1.0 191.0 4.003825833485152 8.704590940604282
phenotype 1 335 31.553476462477843 46.99329427183839

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16997x16997 288898009 262330240
cellular_component_sim 17963x17963 322669369 322651406
disease_sim 4168x4168 17372224 16578192
genetic_interaction_sim 17354x17354 301161316 59571392
interaction_sim 16098x16098 259145604 479348
molecular_function_sim 17335x17335 300502225 300484890
pathway_sim 3828x3828 14653584 159182
phenotype_sim 5077x5077 25775929 25770852
protein_interaction_sim 16098x16098 259145604 479348

Table 3. Filtered similarity matrixes

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process ct 15226x15226 231831076 231831076
biological_process el 16992x16992 288728064 288728064
biological_process ka 16992x16992 288728064 262179894
biological_process rf 16992x16992 288728064 288728064
cellular_component ct 4124x4124 17007376 17007376
cellular_component el 4124x4124 17007376 17007376
cellular_component ka 4124x4124 17007376 17007376
cellular_component rf 4124x4124 17007376 17007376
disease ct 4008x4008 16064064 16064064
disease el 4008x4008 16064064 16064064
disease ka 4008x4008 16064064 15329566
disease rf 4008x4008 16064064 16064064
genetic_interaction el 17354x17354 301161316 301161316
genetic_interaction ka 17354x17354 301161316 59588746
genetic_interaction rf 17354x17354 301161316 301161316
molecular_function ct 7665x7665 58752225 58752225
molecular_function el 7665x7665 58752225 58752225
molecular_function ka 7665x7665 58752225 58752225
molecular_function rf 7665x7665 58752225 58752225
pathway ct 3423x3423 11716929 11703245
pathway el 3423x3423 11716929 8605893
pathway ka 3423x3423 11716929 162557
pathway rf 3423x3423 11716929 8605893
phenotype ct 4597x4597 21132409 21132409
phenotype el 4597x4597 21132409 21132409
phenotype ka 4597x4597 21132409 21132409
phenotype rf 4597x4597 21132409 21132409
protein_interaction ct 16098x16098 259145604 259081193
protein_interaction el 16098x16098 259145604 252047984
protein_interaction ka 16098x16098 259145604 495446
protein_interaction rf 16098x16098 259145604 252047984

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
integration_mean_by_presence ct 19441x19441 377952481 344091976
integration_mean_by_presence el 19525x19525 381225625 364397912
integration_mean_by_presence ka 19525x19525 381225625 293837228
integration_mean_by_presence rf 19525x19525 381225625 364397912
mean ct 19441x19441 377952481 344091976
mean el 19525x19525 381225625 364397912
mean ka 19525x19525 381225625 293837228
mean rf 19525x19525 381225625 364397912

Weight values